Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies
Artikel i vetenskaplig tidskrift, 2018

Bacterial metabolism plays a fundamental role in gut microbiota ecology and host-microbiome interactions. Yet the metabolic capabilities of most gut bacteria have remained unknown. Here we report growth characteristics of 96 phylogenetically diverse gut bacterial strains across 4 rich and 15 defined media. The vast majority of strains (76) grow in at least one defined medium, enabling accurate assessment of their biosynthetic capabilities. These do not necessarily match phylogenetic similarity, thus indicating a complex evolution of nutritional preferences. We identify mucin utilizers and species inhibited by amino acids and short-chain fatty acids. Our analysis also uncovers media for in vitro studies wherein growth capacity correlates well with in vivo abundance. Further value of the underlying resource is demonstrated by correcting pathway gaps in available genome-scale metabolic models of gut microorganisms. Together, the media resource and the extracted knowledge on growth abilities widen experimental and computational access to the gut microbiota.

Författare

Melanie Tramontano

European Molecular Biology Laboratory

Sergej Andrejev

European Molecular Biology Laboratory

Mihaela Pruteanu

Humboldt-Universität zu Berlin

European Molecular Biology Laboratory

Martina Klünemann

European Molecular Biology Laboratory

Michael Kuhn

European Molecular Biology Laboratory

Marco Galardini

Wellcome Trust

Paula Jouhten

European Molecular Biology Laboratory

Aleksej Zelezniak

European Molecular Biology Laboratory

Chalmers, Biologi och bioteknik, Systembiologi

Georg Zeller

European Molecular Biology Laboratory

Peer Bork

Max Delbruck Center for Molecular Medicine

Molecular Medicine Partnership Unit

Julius-Maximilians Universität Würzburg

European Molecular Biology Laboratory

Athanasios Typas

European Molecular Biology Laboratory

K. R. Patil

European Molecular Biology Laboratory

Nature Microbiology

2058-5276 (eISSN)

Vol. 3 4 514-522

Ämneskategorier

Mikrobiologi

Bioinformatik (beräkningsbiologi)

Mikrobiologi inom det medicinska området

DOI

10.1038/s41564-018-0123-9

Mer information

Senast uppdaterat

2018-05-09